.That is the beauty of idioms, Goran -- they mean precisely what they mean, and sometimes for no good reason. Ships that pass in the night are two entities that meet once or erratically.

Ships that pass in the night (from Dictionary.com):

Individuals who are rarely in the same place at the same time. For example, 'Jan works the early shift and Paula the late shift -- they're two ships that pass in the night'. This metaphoric expression comes from Henry Wadsworth Longfellow's poem "The Theologian's Tale" (published in Tales of a Wayside Inn, 1873)._________________Native English teacher at Mister Micawber's

Think of the idiom this way: Two big ocean-going ships -- big freighters, let's say -- pass in the night. One is going one way, and the other is going the opposite way. (I often see this situation not far from my home near Detroit.) They both have a long distance to go, and they both have a job to do. They come near each other just on that one night. They can flash messages to each other, and they are close enough for radio contact. However, they aren't coming to that place to see each other. It was all just coincidence. They are both going somewhere else, and maybe they won't ever pass again.

You can see the same thing in the lives of two students. Maybe the girl is going to a university in Krakow and the guy is going to work in Japan. They meet each other in Rome and have a great time together for a little while. Maybe they even fall in love a little, but she goes back to Krakow and he goes to Japan. Then they are out of sight, and maybe they'll never see each other again.